Coerce to file format structures
These functions coerce a TxDb object to a
GRanges object with
metadata columns encoding transcript structures according to the
model of a standard file format. Currently, BED and GFF models are
supported. If a TxDb is passed to
export, when targeting a BED or GFF file,
this coercion occurs automatically.
## S4 method for signature 'TxDb' asBED(x) ## S4 method for signature 'TxDb' asGFF(x)
x |
A |
For asBED, a GRanges, with the columns name,
thickStart, thickEnd, blockStarts,
blockSizes added. The thick regions correspond to the CDS
regions, and the blocks represent the exons. The transcript IDs are
stored in the name column. The ranges are the transcript bounds.
For asGFF, a GRanges, with columns type,
Name, ID,, and Parent. The gene structures are
expressed according to the conventions defined by the GFF3 spec. There
are elements of each type of feature: “gene”,
“mRNA” “exon” and “cds”. The Name column
contains the gene_id for genes, tx_name for transcripts,
and exons and cds regions are NA. The ID column uses
gene_id and tx_id, with the prefixes “GeneID” and
“TxID” to ensure uniqueness across types. The exons and cds
regions have NA for ID. The Parent column
contains the IDs of the parent features. A feature may have
multiple parents (the column is a CharacterList). Each exon
belongs to one or more mRNAs, and mRNAs belong to a gene.
Michael Lawrence
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(txdb_file)
asBED(txdb)
asGFF(txdb)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.